Quantification Script

1. Introduction
2. Getting Started
3. Command-Line Flags
4. Configuration Files
5. Examples

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Overview

The Quantification Script is designed to process and quantify single-cell data. It allows you to apply various transformations and save histograms or quantified data as CSV files. The scripts expects two files as input, a 'setup.csv' file and a 'standards.csv' file. This manual guides you through the scripts usage and the expected content of the files.

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Getting Started

Linux/Mac

To run the script, navigate to the directory containing the script or enter its absolute location and execute the following command:

python quantification_script.py \
--data_directory path/to/data/ \
--standards_csv path/to/standards.csv \
--setup_csv path/to/setup.csv

Windows

python quantification_script.py ^
--data_directory path\to\data\ ^
--standards_csv path\to\standards.csv ^
--setup_csv path\to\setup.csv

Important Notes

• All the .csv files to be analyzed should be in the --data_directory.
• The --standards_csv and --setup_csv files should be formatted as described in the Configuration Files section.

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Command-Line Flags

--data_directory

• Purpose: Specifies the directory containing the .csv files to be processed.
• Example: --data_directory path/to/data/ (Linux) or --folder path\to\data (Windows)
• Default: None

--standards_csv

• Purpose: Specifies the path to the standards.csv file.
• Example: --standards_csv path/to/standards.csv (Linux) or --folder path\to\standards.csv (Windows)
• Default: None

--setup_csv

• Purpose: Specifies the path to the setup.csv file.
• Example: --setup_csv path/to/setup.csv (Linux) or --folder path\to\setup.csv (Windows)
• Default: None

--save_histograms

• Purpose: When set, saves histograms for each channel specified in setup.csv.
• Example: --save_histograms
• Default: False

--save_channel_data

• Purpose: When set, saves quantified data for each channel as a separate .csv file.
• Example: --save_channel_data
• Default: False

--save_combined_data

• Purpose: When set, saves all quantified data into a single .csv file.
• Example: --save_combined_data
• Default: False

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Configuration Files

setup.csv

This file specifies which channels should be quantified and whether histograms should be created for each channel.

channel	standard	quantify	histogram
Channel_1	Standard_1	1	1
Channel_2	Standard_2	1	1
Channel_3	Standard_3	0	0

• channel: The name of the channel.
• standard: The name of the standard used for quantification. This should match an entry in standards.csv.
• quantify: 1 for 'Yes' and 0 for 'No'.
• histogram: 1 for 'Yes' and 0 for 'No'.

standards.csv

This file contains the standards used for quantifying the channels, specifying the slope and y-axis values.

standard	slope	y-axis
Standard_1	1.52	11.69
Standard_2	2.68	0.70

• standard: The name of the standard.
• slope: The factor by which to divide for quantification.
• y-axis: This field is currently not used but will be integrated in a future update.

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Examples

To run the script and save histograms:

For Linux/Mac

python quantification_script.py \
--data_directory path/to/data/ \
--standards_csv path/to/standards.csv \
--setup_csv path/to/setup.csv \
--save_histograms

For Windows

python quantification_script.py ^
--data_directory path\to\data\ ^
--standards_csv path\to\standards.csv ^
--setup_csv path\to\setup.csv ^
--save_histograms

Replace placeholders like path/to/data or C:\path\to\data with your actual paths and adjust the values as needed.